+Open data
-Basic information
Entry | Database: PDB / ID: 2idu | ||||||
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Title | Structure of M98Q mutant of amicyanin, Cu(I) | ||||||
Components | Amicyanin | ||||||
Keywords | ELECTRON TRANSPORT / blue copper protein / beta sandwich | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Paracoccus denitrificans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.95 Å | ||||||
Authors | Carrell, C.J. / Ma, J.K. / Antholine, W. / Hosler, J.P. / Mathews, F.S. / Davidson, V.L. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Generation of Novel Copper Sites by Mutation of the Axial Ligand of Amicyanin. Atomic Resolution Structures and Spectroscopic Properties Authors: Carrell, C.J. / Ma, J.K. / Antholine, W.E. / Hosler, J.P. / Mathews, F.S. / Davidson, V.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2idu.cif.gz | 60.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2idu.ent.gz | 42.1 KB | Display | PDB format |
PDBx/mmJSON format | 2idu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/2idu ftp://data.pdbj.org/pub/pdb/validation_reports/id/2idu | HTTPS FTP |
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-Related structure data
Related structure data | 2idqC 2idsC 2idtC 1aacS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 11518.104 Da / Num. of mol.: 1 / Mutation: M98Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Gene: mauC, ami / Plasmid: pMEG / Production host: Escherichia coli (E. coli) / References: UniProt: P22364 |
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#2: Chemical | ChemComp-CU1 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.49 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 5.5 Details: 2.6 M phosphate, pH 5.5, EVAPORATION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 / Wavelength: 0.9 Å | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2005 | |||||||||
Radiation | Monochromator: Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 0.95→20 Å / Num. all: 47487 / Num. obs: 47487 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 18.4 | |||||||||
Reflection shell | Resolution: 0.95→0.97 Å / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 10 / % possible all: 37.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1AAC Resolution: 0.95→20 Å / Num. parameters: 8456 / Num. restraintsaints: 10269 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Displacement parameters | Biso mean: 15.253 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 3 / Occupancy sum hydrogen: 793 / Occupancy sum non hydrogen: 933 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.95→20 Å
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Refine LS restraints |
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